Workflow Description

Environment Setup (osx-64)

## Create an environment (Currently on OS)
conda create -n nf -c bioconda nextflow -y;
## Due to arm64 architecture, conda environment created with osx-64
CONDA_SUBDIR=osx-64 conda create -n nf -y;
## Install Relevant packages to assignment
conda activate nf;
conda install -c bioconda -c conda-forge entrez-direct sra-tools fastqc trimmomatic skesa spades pigz tree nextflow fastp csvtk -y;
conda install bioconda::seqkit;

Activate environment

conda activate nf

Two Samples selected that were not previously used in class

• These sample data were located in the test_data/ folder.
• Species: Listeria monocytogenes
• Sample IDs: SRR33049470, SRR33028439

Nextflow Version:

• Nextflow version 24.10.5.5935

Operating System (MacOS) osx-64

• Tools Selected include fastp, skesa, and seqkit
• Fastp was initially ran on raw Fastq sequences. These sequences were downloaded by the commands in cmds.sh.
• After revising and trimming the reads using

Command usage

nextflow workflow_parallel_sequential.nf --reads "test_data/*_{1,2}.fastq.gz"

Workflow Image